Contacts of the helix formed by residues 276 - 283 (chain A) in PDB entry 1HKC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A THR* 1.3 75.2 - - - +
277A PHE* 1.3 81.3 + - + +
278A ASP 3.3 0.2 - - - -
279A ARG* 3.6 15.3 + - - +
280A GLU* 3.1 29.8 + - - +
283A ARG* 5.6 0.2 + - - -
312A LYS* 3.3 39.0 + - - +
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Residues in contact with PHE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TYR* 4.6 9.9 - + - -
26A LEU* 4.1 15.7 - - + -
29A MET* 3.5 20.0 - - + -
275A THR* 3.0 10.0 - - - +
276A GLU* 1.3 102.3 - - + +
278A ASP* 1.3 65.0 + - - +
280A GLU* 3.4 8.5 + - - +
281A ILE* 3.1 23.4 + - - +
305A LEU* 3.7 19.9 - - + +
308A LEU* 3.7 16.8 - - + +
309A ILE* 3.7 41.3 - - + -
312A LYS* 3.9 32.3 - - + -
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Residues in contact with ASP 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ARG* 3.5 24.6 + - + +
275A THR* 2.5 40.1 + - - +
277A PHE* 1.3 78.2 - - - +
279A ARG* 1.3 62.6 + - - +
281A ILE* 3.3 12.3 + - - +
282A ASP* 3.2 20.3 + - - +
295A LYS* 4.6 2.6 - - - +
296A MET* 3.5 16.0 - - + +
305A LEU* 4.0 8.4 - - - +
381A ARG* 2.7 41.7 + - - -
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Residues in contact with ARG 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A GLU* 2.5 55.3 + - - +
274A ARG* 3.1 42.6 + - - +
275A THR* 3.0 25.5 + - - +
276A GLU* 3.9 11.0 - - - +
277A PHE 3.3 0.4 - - - -
278A ASP* 1.3 74.8 - - - +
280A GLU* 1.3 63.7 + - - +
282A ASP* 3.3 5.0 + - - +
283A ARG* 3.1 32.6 + - + +
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Residues in contact with GLU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLU* 3.1 20.8 + - - +
277A PHE* 3.9 9.4 - - - +
278A ASP 3.3 0.2 - - - -
279A ARG* 1.3 73.4 - - - +
281A ILE* 1.3 66.3 + - - +
283A ARG* 3.2 45.2 + - - +
284A GLY* 3.2 10.7 + - - -
308A LEU* 4.1 30.7 - - + +
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A PHE 3.1 11.3 + - - +
278A ASP* 3.5 12.6 - - - +
280A GLU* 1.3 77.5 - - - +
282A ASP* 1.3 64.2 + - - +
284A GLY* 3.6 2.8 + - - -
285A SER* 3.5 17.8 + - - -
295A LYS* 4.2 31.0 - - + +
301A TYR* 4.0 32.0 - - + +
304A GLU* 3.7 29.4 - - + -
305A LEU* 4.2 14.1 - - + -
308A LEU* 3.5 21.9 - - + +
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Residues in contact with ASP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ARG* 4.6 9.3 + - - +
278A ASP 3.2 10.1 + - - +
279A ARG* 3.4 13.2 - - - +
280A GLU 3.1 0.6 - - - -
281A ILE* 1.3 83.1 - - - +
283A ARG* 1.3 61.3 + - - +
285A SER* 2.5 28.3 + - - -
288A PRO* 3.7 8.2 - - - +
289A GLY* 2.8 31.4 + - - -
292A LEU* 3.8 13.1 - - - +
295A LYS* 2.8 34.4 + - + +
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Residues in contact with ARG 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ARG* 3.1 17.0 + - + +
280A GLU* 3.2 47.0 + - - +
282A ASP* 1.3 76.9 - - + +
284A GLY* 1.3 58.9 + - - +
285A SER 3.3 3.9 + - - +
288A PRO* 5.0 7.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il